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Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae

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plant Communications 2024年第7期5卷 68-89页

作者： Jie Liu Shi-Zhao Zhou Yun-Long Liu Bin-Yan Zhao Dongmei Yu Mi-Cai Zhong Xiao-Dong Jiang Wei-Hua Cui Jiu-Xia Zhao Juan Qiu Liang-Min Liu Zhen-Hua Guo Hong-Tao Li Dun-Yan Tan Jin-Yong Hu De-Zhu Li cas key laboratory for plant diversity and biogeography of East Asia&Yunnan key laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Germplasm Bank of Wild Species&Yunnan key laboratory for Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China College of Life Sciences Xinjiang Agricultural UniversityÜrümqi 830052China University of Chinese Academy of Sciences Beijing 100049China These authors contributed equally to this article

Brassicaceae represents an important plant family from both a scientific and economic ***,genomic features related to the early diversification of this family have not been fully characterized,especially upon the uplift of the Tibetan Plateau,which was followed by increasing aridity in the Asian interior,intensifying monsoons in Eastern Asia,and significantly fluctuating daily ***,we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius(Arabodae;clade D)and Tetracme quadricornis(Hesperodae;clade E),together with genomes representing all major Brassicaceae clades and the basal *** reconstructed an ancestral core Brassicaceae karyotype(CBK)containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in *** detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events,which correlate well with the early divergence of core *** identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1(TPS1)gene family,which encodes enzymes with essential regulatory roles in flowering time and embryo *** TPS1s were mainly randomly amplified,followed by expression *** results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

关键词： Cruciferae genomic features ancient hybridization core Brassicaceae karyotype CBK TREHALOSE-6-PHOSPHATE SYNTHASE 1 genes TPS1s

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Predator-prey encounters:deciphering the robbery relationship between highwayman flies and their ant victims

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Integrative Zoology 2024年第2期19卷 253-261页

作者： Ying ZHAO Yulong YU Zhi CHEN Ying LI Huidan TENG Guillaume CHOMICKI Chuntian ZHANG Gao CHEN Yunnan key laboratory for Integrative Conservation of plant Species with Extremely Small Populations KunmingChina cas key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingChina College of Life Science Shenyang Normal UniversityShenyangChina School of Ecology and Environmental Science Yunnan UniversityKunmingChina University of Chinese Academy of Sciences BeijingChina Ecology and Evolutionary Biology School of BiosciencesAlfred Denny BuildingUniversity of SheffieldWestern BankSheffieldUK

Examples of predator–prey interactions in which flies rob ants are *** date,this behavior has only been recorded in the genus Bengalia Robineau-Desvoidy(Bengaliinae,Diptera,Calliphoridae).These predatory flies ambush ants,and rob them of the food or offspring that they are ***,because of the rarity of this behavior,the reasons and consequences(evolutionary advantages)are unknown,and indeed,the behavior has been sometimes considered *** this study,we employed field investigations and behavioral analyses to investigate whether the sex of the fly Bengalia varicolor,or the weight and quality of the food carried by Pheidole nodus ants influenced fly–ant interactions in their natural *** show that food weight and quality influenced the behavior of *** independent of the fly’s *** behavior by the flies was more successful when the food robbed was of high-quality and light in ***,the weight of the food robbed modulated the escape distance the flies could carry *** then may affect the food quality and weight transported by the *** is a novel example of deciphering the relationship between highwayman flies and their ant *** the widespread distribution of Bengalia flies,we suggest that such interspecific predator–prey encounters may shape the robbery interactions and the carrying behavior of further ant species in nature.

关键词： Bengalia kleptoparasitism Pheidole predatory flies robbing

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Genetic characterization of the entire range of Cycas panzhihuaensis (Cycadaceae)

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plant diversity 2020年第1期42卷 7-18页

作者： Siyue Xiao Yunheng Ji Jian Liu Xun Gong key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesNo.132 Lanhei RDPanlong District.KunmingYunnan province650201 China University of Chinese Academy of Sciences No.19AYuquan RoadShijingshan DistrictBeijing100049China

Cycas panzhihuaensis *** & ***(Cycadaceae) is an endangered gymnosperm species endemic to the dry-hot valley of the Jinsha River basin in southwest *** the wild *** population from Panzhihua Cycad Natural Reserve is well protected and its genetic diversity has been well assessed,the genetic characteristics of populations outside the nature reserve,which face larger risks of extinction,remain ***,the population genetics and historical dynamics of this endemic and endangered species have not been examined across its entire *** this study,to analyze the genetic diversity,phylogeographical structure and demographic history of *** from all its seven known locations,we sequenced and compared molecular data from chloroplastic DNA(psbA-trnH,psbM-trnD,and trnS-trnG),single-copy nuclear genes(PHYP,AC5,HSP70,and AAT) from 61 individuals,as well as 11 nuclear micro satellite loci(SSR) from 102 *** found relatively high genetic diversity within populations and high genetic differentiation among populations of ***,which is consistent with the patterns of other Asian inland *** no significant phylogeographical structure was detected,we found that small and unprotected populations possess higher genetic diversity and more unique haplotypes,which revises our understanding of diversity within this species and deserves due *** of demographic dynamics suggest that human activity might be the key threat to *** on the genetic characterization of ***,we propose several practical guidelines for the conservation of this species,especially for the populations with small sizes.

关键词： Cycas panzhihuaensis Conservation Genetic diversity Phylogeography Chloroplast and nuclear DNA Microsatellite

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The first complete plastid genome of Burmannia disticha L. from the mycoheterotrophic monocot family Burmanniaceae

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plant diversity 2018年第5期40卷 232-237页

作者： Liuqing Ma Pengfei Ma Dezhu Li Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China key laboratory for plant diversity and biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201China University of Chinese Academy of Sciences Beijing 100049 China

Burmanniaceae is one major group within the monocot order Dioscoreales that has not had its plastome *** of Burmanniaceae are mostly achlorophyllous,although the genus Burmannia also includes ***,we report sequencing and analysis of the first Burmanniaceae plastid genome from Burmannia disticha L..This plastome is 157,480 bp and was assembled as a circular sequence with the typical quadripartite structure of plant plastid *** plastome has a regular number of potentially functional genes with a total of 111,including 78 protein coding genes,4 ribosomal RNA(rRNA) genes,and 29 tRNA *** ratio of the total length of genic:intergenic DNA is 1.58:1,and the mean length of intergenic regions is 398 bp,the longest being 1918 *** overall GC content of the *** plastome is 34.90%,and the IR regions in *** are more GC rich(39.50%) than the LSC(32.30%) and SSC(28.80%) *** analysis of protein-coding sequences from plastomes of related species in the order Dioscoreales support a clade comprising Burmanniaceae and *** phylogenetic placement is congruent with previous findings based on nuclear and mitochondrial evidence.

关键词： Burrnannia disticha Burmanniaceae Plastome Phylogenetic analysis

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Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme *** a major biodiversity hotspot

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Journal of Integrative plant Biology 2024年第6期66卷 1192-1205页

作者： Santosh Kumar Rana Hum Kala Rana Jacob BLandis Tianhui Kuang Juntong Chen Hengchang Wang Tao Deng Charles C.Davis Hang Sun cas key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Arkansas Biosciences Institute Arkansas State UniversityJonesboroArkansas 72401USA School of Integrative plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14853USA BTI Computational Biology Center Boyce Thompson InstituteIthacaNew York 14853USA cas key laboratory of plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Department of Organismic and Evolutionary Biology HerbariaHarvard UniversityCambridgeMassachusetts 02138USA

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate *** high species diversity in this mountain system has long been attributed to a complex set of factors,and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago(Mya)to the *** our increasing understanding of the temporal mode of speciation,finer-scale populationlevel investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic *** is largely due to the dearth of organismal sampling among closely related species and populations,spanning the incredible size and topological heterogeneity of this *** study dives into these evolutionary dynamics of speciation using genomic and ecomorphological data of Stellera chamaejasme *** identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages,suggesting a more recent diversification(~2.67-0.90 Mya),largely influenced by Pleistocene glaciation and biotic *** factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the *** study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity,necessitating increased conservation efforts.

关键词： cryptic speciation glacial-interglacial Hengduan Mountains north-south migration Stellera chamaejasme

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Phylotranscriptomics of Swertiinae(Gentianaceae)reveals that key floral traits are not phylogenetically correlated

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Journal of Integrative plant Biology 2023年第6期65卷 1490-1504页

作者： Chunlin Chen Brad R.Ruhfel Jialiang Li Zefu Wang Lushui Zhang Lei Zhang Xingxing Mao Ji Wang Dashan He Yue Luo Quanjun Hu Yuanwen Duan Xiaoting Xu Zhenxiang Xi Jianquan Liu key laboratory of Bio-Resource and Eco-Environment of Ministry of Education&State key laboratory of Hydraulics and Mountain River Engineering College of Life SciencesSichuan UniversityChengdu 610065China Department of Ecology and Evolutionary Biology University of MichiganAnn ArborMichigan 48109USA Institute key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on *** traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic *** subtribe Swertiinae(Gentianaceae)comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse *** we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu,representing the range of floral diversity,using data from the nuclear and plastid *** topological conflicts were present between the nuclear and plastome *** of the 15 genera represented by multiple species are polyphyletic in both *** floral traits including corolla type,absence or presence of lobe scales,nectary type,nectary position,and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic *** also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral *** results highlight the complex evolutionary history of this *** phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.

关键词： ancient hybridization floral diversity Gentianaceae phylogenomics Qinghai-Tibet Plateau subtribe Swertiinae

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Conservation and fruit biology of Sichou oak {Quercus sichourensis,Fagaceae)- A critically endangered species in China

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plant diversity 2016年第5期38卷 233-237页

作者： Ke Xia Lei Fan Wei-bang Sun Wen-yun Chen Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of Sciences Kunming Botanical Garden Kunming Institute of BotanyChinese Academy of Sciences key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of Sciences

Several conservation programs have been started for the critically endangered Sichou oak(Quercus sichourensis) since *** programs include detailed field investigations,seedling cultivation and research on the fruit biology of the *** this study,we first report on the five mature individual trees found in our 9-year field *** far,a total of 10 mature individuals have been *** *** trees are healthy and most produce healthy *** of *** are large with dry masses of 8.0-14.0 *** acorns had high moisture contents at collection and died shortly after(7-28 d) when dried with silica *** of Q,sichourensis acorns varied between *** with the acorns from Funing,the acorns collected from Ceheng were bigger,more viable(germination percentage was up to 96%),less sensitive to desiccation,and germinated *** occurs in regions with a distinct 5-6 month dry *** degradation is largely responsible for the rareness of Quercus sichorensis,but desiccation sensitivity of the acorns may also limit the regeneration of the species and potentially lead to its continued *** a species with extremely small populations(PSESP),*** is facing high risk of extinction and should be defined as a Critically Endangered species in the global IUCN Red List.

关键词： Conservation Cyclobalanopsis sichourensis Recalcitrant seed Desiccation-sensitive Germination Asian monsoon system

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Effects of environment and genotype-by-environment interaction on phenotype of Rorippa elata(Brassicaceae),an endemic alpine plant in the Hengduan mountains

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Journal of plant Ecology 2024年第4期17卷 42-55页

作者： Zhi-Qiang Du Yao-Wu Xing Ting-Shen Han cas key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China University of Chinese Academy of Sciences Beijing 100049China State key laboratory of plant diversity and Specialty Crops Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China

Global climate change poses a severe threat to mountain *** plasticity and local adaptation are two common strategies for alpine plant to cope with such *** may facilitate organismal adaptation to contrasting environments,depending on the influences of the environment or genotype or their interacted *** this study,we use an endemic alpine plant(Rorippa elata)in the Hengduan mountains(HDM)to unravel its phenotypic basis of adaptation strategy and evaluate the relative contributions of environment and genotype to its *** transplanted 37 genotypes of *** into two common gardens across low and high elevations(2800 vs.3800 m)during *** fitness-related traits were measured,including flowering probability and glucosinolates(GS)*** estimated the environmental or genotypic contributions to the phenotype and identified the main environmental *** results revealed that both environment and genotype-by-environment interactions contributed to the phenotypes of *** heterogeneity was identified as a key factor that explained 24%of the total phenotypic *** particular,genotypes of the northern HDM showed significantly higher plasticity in flowering probability than those of the southern ***,within the southern HDM,GS content indicated local adaptation to herbivory stresses for *** genotypes along *** conclusion,our results suggest that *** may have adapted to the alpine environment through species-level plasticity or regional-level local *** processes were shaped by either complex topography or interactions between genotype and mountain *** study provides empirical evidence on the adaptation of alpine plants.

关键词： alpine plant common garden genotype-by-environment Hengduan mountains local adaptation phenotypic plasticity

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Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations

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Current Zoology 2021年第4期67卷 361-370页

作者： Zhonglou Sun Pablo Orozco-terWengel Guotao Chen Ruolei Sun Lu Sun Hui Wang Wenbo Shi Baowei Zhang School of Life Sciences Anhui UniversityHefei230601China School of Biosciences Cardiff UniversityCardiffCF103AXUK key laboratory for plant diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming650201China

Climate fluctuations in the past and in the future are likely to result in population expansions,shifts,or the contraction of the ecological niche of many species,and potentially leading to the changes in their geographical *** of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect ***,we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation(ABC)and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate *** results indicated that the suitable habitats for the *** shifted to the Southeast and contracted during the Last Glacial Maximum,whereas they covered a broader more northern position in the Middle *** ABC analyses revealed that the modern *** populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat ***,our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate *** results indicated that the *** diverged in the recent time after the glacial period and simultaneously as its habitat's expanded in the Middle ***,the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution,which has great influence on the Chinese muntjac's population demographic history.

关键词： climate fluctuations.Middle Holocene Muntiacus reevesi spatial dynamics suitable habitat

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A chromosome-level genome assembly reveals that tandem-duplicated CYP706V oxidase genes control oridonin biosynthesis in the shoot apex of Isodon rubescens

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Molecular plant 2023年第3期16卷 517-532页

作者： Yuwei Sun Jie Shao Haili Liu Hua Wang Guangyi Wang Jianhua Li Yaping Mao Zhuo Chen Ke Ma Lin Xu Yong Wang cas-key laboratoryofSynthetic Bioogy CAS Center forEcellenceinMolecular Plant SciencesInsttuteof Plant Physioogy andEoogyChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100039China National key laboratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China

The ent-kaurenoids(e.g.,oridonin and enmein)from the Isodon genus(Lamiaceae)are one class of diterpenoids with rich structural diversity and intriguing pharmaceutical *** contrast to the well-established gibberellin pathway,oxidative modifications diversifying the ent-kaurene skeleton in Isodon have remained undetermined for half a *** we report a chromosome-level genome assembly of ***,a well-recognized oridonin producer long favored by Asian people as a traditional herb with antitumor *** shoot apex was confirmed to be the actual region actively producing ent-kaurene *** comparative genomics and phylogenetic analyses,we discovered a cluster of tandem-duplicated CYP706V oxygenase-encoding genes located on an ancient genomic block widely distributed in eudicots,whereas almost exclusively emerged in Isodon *** the shoot apex,IrCYP706V2 and IrCYP706V7 oxidized the ent-kaurene core in the initial stage of oridonin *** of CYP706Vs in other Lamiaceae plants offered an explanation for the specific kaurenoid production in Isodon ***,we found that the Isodon genomes encode multiple diterpenoid synthases that are potentially involved in generating diterpenoid *** findings provided new insights into the evolution of the lineage-specific diterpenoid pathway and laid a foundation for improving production of bioactive ent-kaurene-type diterpenoids by molecular breeding and synthetic biology approaches.

关键词： oridonin biosynthesis Isodon rubescens genome sequencing CYP706 oxidases diterpenoid diversity

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